[Insight-users] Clarification on itkOrientImageFilter orientationcodes

[Miller, James V (Research)]

Bill recently found a problem with some of the orientation codes
in the OrientImageFilter.  The problems arose on some cases where
two permutations were required.  He discovered if he changed the 
order of the permutations (in these case), he got the
the answer he was expecting.

Unfortunately, these fixes have not been committed back into the
repository.

In the interum, you could edit OrientImageFilter and experiment
with changing the order of permutations for the cases giving 
you problems.

Jim




-----Original Message-----
From: Mark Wyszomierski [mailto:markww at gmail.com]
Sent: Thursday, April 21, 2005 1:18 PM
To: Miller, James V (Research)
Cc: insight-users at itk.org
Subject: Re: [Insight-users] Clarification on itkOrientImageFilter
orientationcodes


I'm experiencing some problems in with image orientation translations
for axial images;

When translating a coronal image to sagittal, everything works as expected:
start w/: RSA
ask for:  ASL
get:       ASL

However, when translating an axial image to sagittal, I'm ending up
with a coronal image instead:
start w/: RAI (or LAS)
ask for:  ASL
get:       IRA (or SLA)

This result is confusing.  Essentially, the RSA=>ASL translation
requires a 90 degree turn clockwise along the y-axis, which itk does
correctly.  Meanwhile, the RAI=>ASL translation requires a 90 degree
turn clockwise around both the x-axis and y-axis.  But it seems for
RAI=>ASL, itk is instead rotating 90 degrees clockwise along the x-
and *z-axis* which results in a coronal image of IRA rather than a
sagittal of ASL...   any idea why this is happening?

In attempting to work around the problem, I pretended that my axial
image (RAI) was instead a coronal image (RSA).  I instructed itk to
translate the image to ARS (an unorthodox axial image) which
essentially is asking itk to rotate the image 90 degrees clockwise
around the x-axis and y-axis; the same as an RAI=>ASL translation
would ask.  This translation did indeed result in the expected output
of an ASL image.

Can anyone shed light onto the problems w/ translating axial to
sagittal?  thanks,

Mark

On 4/21/05, Miller, James V (Research) <millerjv at crd.ge.com> wrote:
> For DICOM files, you would need to calculate codes from the
> ImageOrientationPatient and not the ImagePositionPatient.
> 
> The codes in the OrientImageFilter label the "start" of the
> row, column, slices.  So in that nomenclature, your Desired
> orientation would probably be ASL.
> 
> Bill Lorensen has been working on some changes to the OrientImageFilter
> so that it will automatically set the Given orientation from the
> direction cosines of the image (ImageOrientationPatient), so the user
> would only have to specify the Desired orientation.  He is also
> adding convenience methods so that the user can simply request
> Axials, Coronals, or Sagittals instead of having to specify
> the codes.
> 
> It doesn't look as though his changes to the OrientImageFilter
> have been checked in yet.  But he is close to having it ready
> for committing to the repository.
> 
> Jim
> 
> 
> -----Original Message-----
> From: insight-users-bounces at itk.org
> [mailto:insight-users-bounces at itk.org]On Behalf Of Mark Wyszomierski
> Sent: Thursday, April 21, 2005 9:45 AM
> To: insight-users at itk.org
> Subject: [Insight-users] Clarification on itkOrientImageFilter
> orientationcodes
> 
> Hello all,
> 
> I implemented the itkOrientImageFilter so I can snap all my volumes to
> a particular orientation.The input/output is working, I am just unsure
> of what the orientation codes mean. For instance, I would like all my
> images to have their rows going towards the Posterior, columns going
> towards the Feet, and the Z (slice direction) going towards the Right
> side of the patient. How do I translate that into the codes provided
> by the filter?
> 
> Also, since my input are DICOM files, can I translate the
> ImagePositionPatient tag directly to one of the filter codes?
> 
> Thanks for any clues,
> Mark
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